[Genome] HPRD data in GeneSorter

Wed Apr 16 05:03:28 PDT 2008

Hi Galt,

This is huge help; thanks so much. I think what I had done is
associate uc001hbr.1 with UBE3C in error on the UCSC browser. When
typing in UBE3C in HPRD I then got a different set of results which
gave rise to the confusion. Thanks again.

-b

On Tue, Apr 15, 2008 at 11:34 PM, Galt Barber <galt at soe.ucsc.edu> wrote:
>
>  When I go to HPRD, I see pretty much the same list
>  of interactions there that we have, which is what
>  one would expect.
>
>  http://www.hprd.org/interactions?protein=01826&isoform_id=01826_1&isoform_name=
>
>  Name of Interactor              Experiment Type                 Type
>  Nuclear transcription factor Y, beta    In Vivo ; Yeast 2 Hybrid Direct
>  L1 cell adhesion molecule               In Vitro                Direct
>  Neurocan                In Vitro                Direct
>  Contactin associated protein like 2             In Vitro         Direct
>  Contactin 1             In Vitro                Direct
>  NRCAM           In Vitro                Direct
>  Vac14 homolog           In Vivo ; In Vitro ; Yeast 2 Hybrid       Direct
>
>  The only one that HPRD has that we don't have is Vac14 homolog,
>  and I think that it is because we don't have that in our knownGenes,
>  so GeneSorter has nothing to map to.
>
>  I got this by going to GeneSorter, choosing Human,
>  entering "uc001hbr.1" in the search,
>  going to configure columns, checking HPRD P2P to turn on the column,
>  and then back on the main view, selecting HPRD Protein-to-Protein
>  from the dropdown sort-by list.
>  I see the seven things you listed in your attachment,
>  exactly the same way.
>
>  I click the top link CNTN2 in the HPRD P2P column to go to HPRD site.
>   http://www.hprd.org/protein/01826
>
>  I selected the "Interactions" tab.
>  If you read the genes, they look the same as in GeneSorter.
>  Does that answer your question?
>
>  The link you showed
>
> > http://www.hprd.org/interactions?protein=15604&isoform_id=15604_1&isoform_name=
>
>  is Ubiquitin protein ligase E3C
>  which I don't think is associated with
>  Contactin 2 (uc001hbr.1) at all.
>
>  Hope that helps!
>
>  -Galt
>
>
>  On Sat, 12 Apr 2008, Brett Abrahams wrote:
>
>  > Hi Galt,
>
>
> >
>  > I was hoping you might be able to answer a follow-up question
>  > regarding a specific example - UBE3C (aka uc001hbr.1).
>  >
>  > Using HRPD, and limiting the distance score to 1.5 or less, I observe
>  > seven interactors (see attached and
>  > http://genome.ucsc.edu/cgi-bin/hgNear?hgsid=106065993).
>  >
>  > When I go directly to the HPRD, however, only four interactions are
>  > reported and none of these overlap with those listed on the UCSC site.
>  > http://www.hprd.org/interactions?protein=15604&isoform_id=15604_1&isoform_name=
>  >
>  > I've look through the faqs and the 2 references listed on the HPRD
>  > site but nothing seems to clear things up. I love this tool (and your
>  > link to the data) but do want to make sure I know what the output
>  > means. Any thoughts would be much appreciated. Thanks in advance.
>  >
>  > -b
>  >
>  > On Fri, Jan 11, 2008 at 5:03 PM, Galt Barber <galt at soe.ucsc.edu> wrote:
>  > >
>  > >  If you are interested in the HPRD P2P interaction distance column,
>  > >  you can see it's desciption page here:
>  > >
>  > >  http://genome.ucsc.edu/cgi-bin/hgNear?hgsid=102348218&near.do.colInfo=hprdP2p
>  > >
>  > >  We filtered out paths of length greater than two
>  > >  because of exponential growth of lower-value interaction paths.
>  > >
>  > >  Our length 1 (and 0) paths should correspond to what you see
>  > >  on the HPRD site, and the other (71 - 8 = 63) paths would probably
>  > >  be interactions between those 8 and other proteins, for
>  > >  a length of 2.  Without knowing the gene and assembly you
>  > >  were looking at, this is just my speculation.
>  > >
>  > >  If you want more details about the exact construction
>  > >  of our p2p paths, you would need to look at our make-docs.
>  > >
>  > >  We also have p2p interaction data from the E. Vidal and M. Wanker studies.
>  > >
>  > >  -Galt
>  > >
>  > >
>  > >
>  > >
>  > >  On Fri, 11 Jan 2008, Edward Herman wrote:
>  > >
>  > >  > Hi,
>  > >  > We have recently used the Gene Sorter tool on our gene of interest, and
>  > >  > found a striking overlap between the list that this tool generated and our
>  > >  > own data.  We would like to know more about what publications or results the
>  > >  > Gene Sorter is based on and how we can access them.  In particular, we are
>  > >  > interested in the HRPD Protein-Protein interaction database.  We tried their
>  > >  > website (www.hprd.org) searching on our gene and clicking the "Interactions"
>  > >  > tab, but only a subset (8 out of 71) appear here with links to publications.
>  > >  >
>  > >  > Can you tell us more about what data was used to generate the HRPD
>  > >  > Protein-Protein interaction database on the Gene Sorter tool?
>  > >  >
>  > >  > Thanks,
>  > >  > Eddie
>  > >  > Geschwind Lab, UCLA
>  > >
>  > >
>  > > > _______________________________________________
>  > >  > Genome maillist  -  Genome at soe.ucsc.edu
>  > >  > http://www.soe.ucsc.edu/mailman/listinfo/genome
>  > >  >
>  > >
>  >
>  >
>  >
>  > --
>  > Brett S. Abrahams, PhD
>  > Program in Neurogenetics & Department of Neurology, UCLA
>  > Room 2309, Gonda Neuroscience and Genetics Research Center
>  > 695 Charles Young Dr South, Los Angeles, CA 90095
>  > Lab: (310) 794-7537 Cellular: (310) 347-9060
>  > Fax: (866) 892-6444
>  >
>  > http://myprofile.cos.com/abrahams
>  >
>

-- 
Brett S. Abrahams, PhD
Program in Neurogenetics & Department of Neurology, UCLA
Room 2309, Gonda Neuroscience and Genetics Research Center
695 Charles Young Dr South, Los Angeles, CA 90095
Lab: (310) 794-7537     Cellular: (310) 347-9060
Fax: (866) 892-6444

http://myprofile.cos.com/abrahams